Full-text extraction pipeline for ALD process parameters (v2.1)

Abstract

Code that builds the ALD process parameter database (v2.1) from the scientific literature: corpus retrieval and full-text acquisition, topical screening, extraction of eight process parameters from the complete article text with an open-weight large language model, per-field value selection and a second pass over empty fields, deterministic recovery of provenance spans, evaluation against a frozen held-out benchmark, and figure generation. Two scoring codes are released. scorer_fixed.py is the frozen code used for the earlier evaluation of this corpus. 21_scorer_aligned.py corrects three defects found in it: temperatures reported in kelvin were compared without conversion, chemical names were compared without alias resolution, and the numeric parser took digits from chemical formulae. The third defect applies to the gold annotations as well as to the predictions. Every score in the accompanying manuscript is reported under both codes. Version 2.1 adds the analysis stage that produced the numbers and figures of the current manuscript, which the version 2.0 package did not contain. It also adds 92_repair_gold.py, which reproduces the correction of the gold standard released as version 1.1 of that file and writes a row-by-row report of what was re-paired, and 91_annotator_agreement.py, which computes agreement between the two annotators. The evaluation split shipped in 06_evaluation is the corrected 83-article split. The regular-expression and named-entity extractors of the earlier version of this pipeline are retained as the comparison baseline, not as the production extractor. 10_analysis_v7/32_consistency_check_v7.py recomputes every number reported in the manuscript from the released files and checks it against the manuscript text. Accompanying dataset: ALD process parameter database v2.1, deposited separately under CC BY 4.0 at https://doi.org/10.5281/zenodo.22653094.